Sequence
atgc intronic sequence ATGC exonic sequencegttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 8
gttagtaaccccccttgaacttca----gtaacatt-attgttgattagaaggcaatgctt----agattttatcatttctaatggctacaaacattttaagtttattta----ttggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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gttagtaaccccc-ttgcacttcctaatggaacatttatcattgtttagaaggaaatgttcgatggaattaaaaagttgcaaatgtttgaagttaatttttatatggataaaatttgcacaagctgttctctaaaataaagtgcgcattctgtgcagATTTGAGGAGCATGAGGCACCTGGATCGAGATCCTTTTTTACAGAGATAATTGCATCGGTTTCAGATATAAAATTTGCAAGGGATGGAAGGCACATTCTT
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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------------------------------------ttgcatacaaggaaaaccat---ttttctggagccta----ttatatatgtattcatttatgtgatttgttttgcggtaaactcacagaa-tattaccttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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----------------------------------ttttgcatacaaagaaaagcat---ttttctggatcctattatatttattcattt-atgtgatttcttttgcggtagactcacagaaaattatt------ttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------gttagtaaccccccttgaacttcagt-aacattattgt-tgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagttta---tttattggtcatggtcttatctggttta--actggggcatcttgtt-cagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
gttagtaacccc-----ccttga--acttcagtaacattattgttgattaga------aggcaatgcttagattttatcatttctaatggctacaa----acattttaagtttatttat-tgg--tcatggtct----tatctggtttaactggggcatc--ttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatct-tgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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--------------------------------tgcattgatcagggaaaaagaaaaaaaaa--atcattttgaagg----taaacgtttt-----tatttagtgctctt--tcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
upper sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 8
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttc-taatggctacaaac---attttaagtttatttattggtcatggt--cttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
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--------------------------------------------tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgg------gtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|211227826|gb|FL399539.1|FL399539EST: CGGCTTATTGATCTGCGACAGTCAGCACTGTGTGACAACCATGCTAAACT ATTTGAGGAGCATGAAGCACCTGGGTCAAGATCCTTTTTTACAGAGATAAT
genomic: CGGCTTATTGATCTGCGACAGTCAGCACTGTGTGACAACCATGCTAAACTgttagtaacc ... tcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAAT
EST:
gi|71772341|gb|DR970277.1|DR970277EST: CGGCTTATTGATCTGCGACAGTCAGCACTGTGTGACAACCATGCTAAACT ATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAAT
genomic: CGGCTTATTGATCTGCGACAGTCAGCACTGTGTGACAACCATGCTAAACTgttagtaacc ... tcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
gtttaac putative branch site (score: 3)
tcttgttc putative PPT
ttatttatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
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gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
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